Identifying circRNA-associated-ceRNA networks in the hippocampus of Aβ1-42-induced Alzheimer's disease-like rats using microarray analysis

Wang, Zhe; Xu, Panpan; Chen, Biyue; Zhang, Zheyu; Zhang, Chunhu; Zhan, Qiong; Huang, Siqi; Xia, Zian; Peng, Weijun

doi:10.18632/aging.101427

Cited by 82 publications

(67 citation statements)

References 41 publications

(39 reference statements)

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“…Recently, it has been demonstrated that circRNAs play a role in both cellular senescence and cellular survival [ 27 ]. From a wide range of organisms, including C. elegans [ 13 ], Drosophila [ 12 ], mice [ 10 ], rats [ 28 ], monkeys [ 11 ], tree shrews [ 29 ], and pigs [ 30 ], a large number of circRNAs significantly changed during aging were identified. For example, the accumulation of circRNAs in the brain was discovered across different species compared to their linear isoforms [ 10 , 13 , 23 , 29 ].…”

Section: Discussionmentioning

confidence: 99%

Identification and characterization of human ovary-derived circular RNAs and their potential roles in ovarian aging

Cai

et al. 2018

Aging

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Circular RNAs (circRNAs) have recently been shown to exert effects on multiple pathological processes by acting as miRNA sponges. However, the roles of circRNAs in ovarian senescence are largely unknown. The objective of this study was to identify the circRNAs involved in ovarian aging and predict their potential biological functions. We first performed RNA-sequencing to generate ovarian circRNA expression profiles from young (n = 3) and aging (n = 3) groups. In total, 48,220 circRNAs were identified, of which 194 circRNAs were significantly up-regulated and 207 circRNAs were down-regulated during aging (fold change > 2, P < 0.05). Bioinformatics analysis demonstrated that the metabolic process, regulated secretory pathway, oxidation-reduction process, steroid hormone biosynthesis, and insulin secretion pathways, which may be associated with ovarian aging, were significantly enriched (P < 0.05). The biological characteristics of ovary-derived circRNA, such as back-splicing, RNase R resistance, stability, and alternative splicing, were further validated. Bioinformatics predicted that most of the circRNAs harboured miRNA binding sites, of which circDDX10-miR-1301-3p/miR-4660-SIRT3 axis may be involved in the regulation of ovarian function. Our study indicates that circRNAs are aberrantly expressed in the aging ovary and may play potential roles in the development of ovarian senescence.

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“…Recent studies have found that circRNAs may play crucial roles in neurological diseases, such as Alzheimer’s disease (AD) ( Zhao et al, 2016 ; Sekar et al, 2018 ; Wang et al, 2018 ; Dube et al, 2019 ). Additionally, Zhang et al (2017) characterized circRNA-associated ceRNA networks in senescence-accelerated mouse prone 8 brain and found that these networks could affect the diagnosis and therapy of AD in the near future.…”

Section: Introductionmentioning

confidence: 99%

Correlation Between Plasma CircRNA-089763 and Postoperative Cognitive Dysfunction in Elderly Patients Undergoing Non-cardiac Surgery

Zhou

Li²,

et al. 2020

Front. Behav. Neurosci.

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In our previous experiment, we found that there were abnormal levels of circRNA-089763 in the plasma exosomes of patients with postoperative cognitive dysfunction (POCD) after cardiac surgery. Therefore, the aim of this study was to further investigate the relationship between plasma circRNA-089763 level and POCD in elderly patients after non-cardiac surgery. A prospective cohort study was conducted to select elderly patients undergoing elective non-cardiac surgery. A total of 72 patients were enrolled in this study, and cognitive functions were assessed 1 day before and 3 days after surgery by a series of neuropsychological measurements. Next, patients were divided into POCD and non-POCD (NPOCD) groups according to the Z score method. Blood was collected the day before and 3 days after surgery, and the plasma circRNA-089763 level was detected by quantitative real-time polymerase chain reaction (qRT-PCR). Then, the difference and correlation in plasma circRNA-089763 levels between the POCD and NPOCD groups were analyzed. On the third day after surgery, the incidence of POCD was 30.56%. The relative level of circRNA-089763 in the POCD group was 2.41 times higher than that in the NPOCD group ( t = 4.711, p < 0.001), patients in POCD group had higher age ( t = 5.971, p < 0.001), higher American Society of Anesthesiologists classification (χ 2 = 14.726, p < 0.001), less years of education ( t = 2.449, p = 0.017), more intraoperative blood loss ( t = 3.196, p = 0.002), and higher visual analog scale (VAS) scores ( t = 10.45, p < 0.001). The binary logistic regression analysis showed that the circRNA-089763 level, age, and intraoperative blood loss were independently associated with POCD (OR: 2.75, 95% CI: 1.261–5.999, p = 0.011; OR: 1.32, 95% CI: 1.114–1.565, p = 0.001; OR: 1.017, 95% CI: 1.004–1.03, p = 0.011). These results demonstrated that the circRNA-089763 plasma level was related to POCD after non-cardiac surgery in elderly patients.

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“…Recently, circRNAs have been shown to act as microRNA (miRNA) sponges to regulate gene expression and function in many biological processes [ 16 , 22 ]. Sometimes, one circRNA could harbor multiple miRNA-binding sites and inhibit miRNA activity to bind mRNA targets to serve as competing endogenous RNAs (ceRNAs) [ 21 , 23 ]. However, only a few circRNAs contain multiple binding sites to trap one particular miRNA [ 24 ], and the function of circRNA remains largely unknown.…”

Section: Introductionmentioning

confidence: 99%

Circular RNA and mRNA profiling reveal competing endogenous RNA networks during avian leukosis virus, subgroup J-induced tumorigenesis in chickens

Qiu

Chang

et al. 2018

PLoS ONE

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Avian leukosis virus subgroup J (ALV-J) can induce myeloid tumors and hemangiomas in chickens and causes severe economic losses with commercial layer chickens and meat-type chickens. Here, we generated ribominus RNA sequencing data from three normal chicken spleen tissues and three ALV-J-infected chicken spleen tissues. Structure analysis of transcripts showed that, compared to mRNAs and lncRNAs, chicken circRNAs shared relatively shorter transcripts and similar GC content. Differentially expression analysis showed 152 differentially expressed circRNAs with 106 circRNAs up regulated and 46 circRNAs down regulated. Through comparing differentially expressed circRNA host genes and mRNAs and performed ceRNA network analysis, we found several tumor or immune-related genes, in which, there were four genes existed in both differentially expressed mRNAs and circRNA host genes (Dock4, Fmr1, Zfhx3, Ralb) and two genes (Mll, Aoc3) involved in ceRNA network. We further characterized one exon-intron circRNA derived from HRH4 gene in the ceRNA network, termed circHRH4, which is an abundant and stable circRNA expressed in various tissues and cells in chicken and localizes in cytoplasm. Our results provide new insight into the pathology of ALV-J infection and circRNAs may also mediate tumorigenesis in chicken.

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“…Non-coding RNAs (ncRNAs) can cause changes in gene expression and the production of proteins and they are involved in the pathology of many neurodegenerative diseases. A recent study used microarray analysis to characterize the expression patterns of circular RNAs (circRNAs), miRNAs and mRNAs in hippocampal tissue from an Aβ1-42-induced AD rat model, and found that a total of 555 circRNAs, 183 miRNAs, and 319 mRNAs were significantly dysregulated (change ≥2-fold and p -value < 0.05) in the hippocampus ( Wang et al, 2018 ). In this section, we discuss three aspects of the relationship between ncRNAs and AD.…”

Section: Non-coding Rna Regulationmentioning

confidence: 99%

The Epigenetics of Alzheimer’s Disease: Factors and Therapeutic Implications

2018

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Alzheimer’s disease (AD) is a well-known neurodegenerative disorder that imposes a great burden on the world. The mechanisms of AD are not yet fully understood. Current insight into the role of epigenetics in the mechanism of AD focuses on DNA methylation, remodeling of chromatin, histone modifications and non-coding RNA regulation. This review summarizes the current state of knowledge regarding the role of epigenetics in AD and the possibilities for epigenetically based therapeutics. The general conclusion is that epigenetic mechanisms play a variety of crucial roles in the development of AD, and there are a number of viable possibilities for treatments based on modulating these effects, but significant advances in knowledge and technology will be needed to move these treatments from the bench to the bedside.

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“…Ordinarily, GN inference algorithms take gene expression datasets, e.g., microarrays or RNA-Seq, as input for the generation of the gene-gene interactions [6,7,15]. These datasets have been massively generated over the last decade for the study of some type of biological process or specific disease [16], allowing the identification of relationships between DNA, RNA, proteins and other gene products. Researchers may then perform computer analysis on this type of data before checking the results in the laboratory.…”

Section: Introductionmentioning

confidence: 99%

Computational Inference of Gene Co-Expression Networks for the identification of Lung Carcinoma Biomarkers: An Ensemble Approach

Delgado-Chaves

Divina

García-Torres

et al. 2019

Genes

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Gene Networks (GN), have emerged as an useful tool in recent years for the analysis of different diseases in the field of biomedicine. In particular, GNs have been widely applied for the study and analysis of different types of cancer. In this context, Lung carcinoma is among the most common cancer types and its short life expectancy is partly due to late diagnosis. For this reason, lung cancer biomarkers that can be easily measured are highly demanded in biomedical research. In this work, we present an application of gene co-expression networks in the modelling of lung cancer gene regulatory networks, which ultimately served to the discovery of new biomarkers. For this, a robust GN inference was performed from microarray data concomitantly using three different co-expression measures. Results identified a major cluster of genes involved in SRP-dependent co-translational protein target to membrane, as well as a set of 28 genes that were exclusively found in networks generated from cancer samples. Amongst potential biomarkers, genes N C K A P 1 L and D M D are highlighted due to their implications in a considerable portion of lung and bronchus primary carcinomas. These findings demonstrate the potential of GN reconstruction in the rational prediction of biomarkers.

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Identifying circRNA-associated-ceRNA networks in the hippocampus of Aβ1-42-induced Alzheimer's disease-like rats using microarray analysis

Cited by 82 publications

References 41 publications

Identification and characterization of human ovary-derived circular RNAs and their potential roles in ovarian aging

Correlation Between Plasma CircRNA-089763 and Postoperative Cognitive Dysfunction in Elderly Patients Undergoing Non-cardiac Surgery

Circular RNA and mRNA profiling reveal competing endogenous RNA networks during avian leukosis virus, subgroup J-induced tumorigenesis in chickens

The Epigenetics of Alzheimer’s Disease: Factors and Therapeutic Implications

Computational Inference of Gene Co-Expression Networks for the identification of Lung Carcinoma Biomarkers: An Ensemble Approach

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